The Isipingo River and Estuary system located in the province of KwaZulu-Natal, although relatively small, has been subjected to the impacts of intense development within the catchment. The catchment is characterized by informal and formal dwellings and intensive industrial activities in the lower catchment and in close proximity to the estuary. Significant modifications to the hydrology of the system has occurred as a result of the diversion of the Umlazi River (which previously merged with the Isipingo River at the estuary mouth), canalization of the lower portion of the Isipingo River flowing through the Prospecton Industrial Area and the development of the Diversion Works system (to regulate flows to the lower Isipingo River), removal of riparian vegetation, encroachment onto the river and estuarine floodplain, and land reclamation through the infilling of wetlands all of which has culminated in a deterioration of the functionality and health of this system. The main aspects of this study focus on water and sediment quality, material flux between the estuary and the sea and the management of the system. The water quality variables covered as part of this dissertation include physical, chemical (nutrients and heavy metals) and microbiological (faecal coliforms) components. The water quality of the river and estuary presents a risk to human health and the concentrations of heavy metals generally exceeded the South African Water Quality Guidelines that prescribes target levels, implying potential negative impacts to aquatic health. The Isipingo system exhibited signs of eutrophication with phosphorus concentrations in excess of the target level to prevent eutrophication. Excessive water hyacinth growth was visible during most of the field surveys. A geochemical assessment of heavy metals in surface sediments of the river and estuary was also undertaken. The results indicate that although the presence of several metals were undetectable at certain river sites, the concentrations of those heavy metals present increased in a longitudinal direction from the river to the estuary. The contamination factor analysis for all metals indicated low contamination except for selenium. The riverine sites yielded moderate enrichment by some heavy metals in both seasons. The degree of contamination for each site with the exclusion of selenium was low. The inclusion of selenium in the assessment raises the estuary to a considerably contaminated status in the wet season. The analysis suggests that the enrichment of the system by selenium is due to an anthropogenic source. The Geo-accumulation Index places the sediment in an overall unpolluted category. The study conducted on the net exchange of heavy metals and nutrients between the Isipingo Estuary and the adjacent marine environment (i.e. Indian Ocean) demonstrates that significant quantities of the suite of heavy metal analysed are exported on an annual basis while copper, nickel and zinc are imported into the estuary. Significant quantities of ammonia and nitrates are exported annually from the Isipingo Estuary while a net annual import of phosphorous is observed. The variation in the quantity and concentration of nutrients exported during the seasons may be attributed to anthropogenic source. The import of nutrients from marine sources can accumulate in the estuary and contribute to eutrophication of the Isipingo Estuary. This study also demonstrated that although the ebb flow has a much longer duration than the flood flow, the flood velocities observed were generally greater than the ebb velocities. The final part of this research identifies other environmental problems experienced in the Isipingo catchment. The following issues are identified as directly or indirectly contributing to stress and deterioration of the water quality of the Isipingo system: reduction in water quantity, poor water quality, moderate enriched sediment, loss of habitat integrity, species diversity and invasive alien vegetation and uncontrolled solid waste. A Water Quality Management Plan including management objectives, strategies and action plans to address the direct and indirect factors influencing the system are proposed. A water quality monitoring program is also proposed for the Isipingo River and Estuary. The adoption and execution of the water quality management plan and monitoring program will assist in the prevention of further degradation of the system and will be a stepping stone toward improvement. / Thesis (M.Sc.)-University of KwaZulu-Natal, Westville, 2013.